sak(1)

Usage

sak [OPTIONS] [-o OUT. fa,fq] IN. fa,fq

Overview

"It slices, it dices and it makes the laundry!"

Original SAK tool by David Weese. Rewrite by Manuel Holtgrewe.

Required arguments

IN INPUT_FILE: Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

Options

-h, --help: Display the help message.

--version: Display version information.

Output Options:

-o, --out-path OUTPUT_FILE: Path to the resulting file. If omitted, result is printed to stdout in FastQ format. Valid filetypes are: .sam[.*], .raw[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

-rc, --revcomp: Reverse-complement output.

-l, --max-length INTEGER: Maximal number of sequence characters to write out.

Filter Options:

`-s, --sequence List of INTEGER's`	Select the given sequence for extraction by 0-based index.
`-sn, --sequence-name List of STRING's`	Select sequence with name prefix being NAME.
`-ss, --sequences List of STRING's`	Select sequences from-to where from and to are 0-based indices.
`-i, --infix List of STRING's`	Select characters from-to where from and to are 0-based indices.

-ll, --line-length INTEGER: Set line length in output file. See section Line Length for details. In range [-1..inf].

Line length

You can use the setting --line-length for setting the resulting line length. By default, sequences in FASTA files are written with at most 70 characters per line and sequences in FASTQ files are written without any line breaks. The quality sequence in FASTQ file is written in the same way as the residue sequence.

The default is selected with a --line-length value of -1 and line breaks can be disabled with a value of 0.

Usage examples

sak -s 10 IN.fa: Cut out 11th sequence from IN.fa and write to stdout as FASTA.

sak -ss 10-12 -ss 100-200 IN.fq: Cut out 11th up to and including 12th and 101th up to and including 199th sequence from IN.fq and write to stdout as FASTA.

Releases

6 releases since Debian 8 (Jessie); the text changed 2 times.

--help since Debian 10 (Buster); --line-length since Debian 10 (Buster); --max-length since Debian 10 (Buster); --out-path since Debian 10 (Buster); --revcomp since Debian 10 (Buster); --version since Debian 10 (Buster); -h since Debian 10 (Buster); -l since Debian 10 (Buster); -ll since Debian 10 (Buster); -o since Debian 10 (Buster); -rc since Debian 10 (Buster).